1 Introduction

Origin: Something to work on before I had full access to lab (aka covid project).

Goals:

  1. Phylogenomic analysis of Phaeocystis
  • Does a phylogenomic approach recapitulate taxonomies derived from the 18S gene?
  1. Genomic biogeography of Phaeocystis
  • Do metagenomic data reveal finer-scale biogeographic patterns in Phaeocystis global distribution?
  • Is there geographic differentiation at the strain, sub-strain, or snp level?
  1. Functional biogeography of Phaeocystis
  • Do metatranscriptomic data show biogeographic patterns in Phaeocystis gene expression?
  • Is expression of certain genes linked to locations or environmental conditions?

Background:

Phaeocystis is a globally occurring haptophyte phytoplanktom genus that causes algal blooms in many locations. Blooms are often considered nuisance blooms or harmful blooms due to large amounts of sulfur-based molecules produced, as well as seafoam.

In addition to being a fascinating and ecologically important phytoplankton genus, Phaeocystis is a good test case for probing the limits of tara data since we have a priori knowledge about where species should be found.

18S v4-based distribution pattern of Phaeocystis species.

2 The data

  • 2 jgi geneomes
  • 4 MMETSP transcriptomes
  • 3 transcriptomes sequences as part of my thesis research

2.0.1 BUSCO

2.0.2 Orthogroups

2.0.3 Tree

Fasttree based on 61 single-copy core genes:

this phylogeny perfectly matches the 18S-gene-based phylogeny.

2.1 Tara Read Mapping

2.1.1 Against all genes:

a.k.a. the stumbling block

Inconcistent patterns between data-types:

  • P. antarctica is more dominent in metaG data (jgi genome and caron isolate MMETSP)
  • P. antarctica genes that recruit in the N. atlantic and are annotated are also annotated in the other species data
  • P. globosa ccmp1528 overwhelmingly recruits the majority of the metaT reads

2.1.2 Against single-copy core genes (SCGs):

  • P. jahnii really pops out in this analysis
  • the situation is improved in the metaT 0.8-5 µm size fraction … but not the others

2.2 Intercomparison between data types

SMALL size fraction

3 Micromonas

Another globally distributed phytoplankton genus. Sanity check!

3.1 Data

  • 2 jgi genomes
  • 4 MMETSP transcriptomes

3.2 tree

## busco

3.3 Tara Read Mapping

- Inconsistency again - MMETSP1327 pops out in metaT, but not the G v T pattern as much as in the Phaeocystis results

3.4 Intercomparison between data types

4 Conclusions

  • Species and strain level biogeographical patterns may beyond the scope of analyses possible with Tara meta ’omic data?

  • Seasonal/temporal variation in sampling may play role in confounding patterns?

5 Outlook

Pre-Antarctica:

  • finish vitamin trial (thanks for all the help so far!!!)
  • P. pouchetii reference transcriptome sequencing

In Antarctica

  • wirte P. globosa microbiome paper
  • collect samples fpr metaT to complement Van Mooy lipidomic samples, collect surface water flowthrough transects for metaT/metaP, collect P. antarctica colonies for microbiome analysis and new cultures, trace metal (iron and B12) bottle enrichment experiment

Post Antarctica:

  • RNA and protein extractions from cruise and year one of CCB time series
  • start P. pouchetii and P. antarctica microbiome experiments